Through Darkness
by ShivaVixen
Summary: "A good friend is a connection to life - a tie to the past, a road to the future, the key to sanity in a totally insane world." Lois Wyse. It starts with a murder on a diplomatic mission to Babel to discuss the alliance between the Federation and Klingon Empire, and turns into a game of intrigue, treason and secret agents that might just destroy them all ...
1. Chapter 1

**Hello, my beloved readers- This is the sequel to In Need and Deed and True Friendship. I would recommend reading those first, along with the three oneshots that set up my unique universe, otherwise none of this will make sense. (I realized that all I had to do to add this story was rewrite one line at the end of True Friendship- so I will be editing that in upcoming weeks.)**

 **As you can guess, I am going to be doing a rewrite of Into Darkness. However, like True Friendship, which was a rewrite of ST: 2009, it will be different. Very Different, as I pretty drastically altered the first one … so, only a few plot elements will remain the same. Some mention of TOS events happening in this timeline- or rather, TOS Characters meeting earlier and very different fates happening to them …**

 **Also, I would have had this up sooner, but, well, the death of Nimoy really killed my inspiration. However, as this is fanfiction, Spock Prime, Alias Selek, will still be here for, at the least, a bit longer.**

 **Warnings: This is a FRIENDSHIP fic. That means NO ROMANTIC FOCUS.**

" **Alien Language translated to English.** "

" _Foreign earth language translated to English._ "

"Occasionally, a _Foreign/Alien word_ will be in a sentence."

"Speaking through a Communicator will be underlined."

' _Telepathic speech.'_

 _Thoughts._

* * *

" **The best time to make friends is before you need them." ~Ethel Barrymore**

* * *

In Riverside, Iowa, the sun was shining, the new Academy finally had the dorms completed, and Admiral Pike was suffering a headache.

The cause of the headache was standing in front of him, accompanied by his First/Science officer, and looking unrepentant.

"Kirk, while the story of black cats and transmuters was fascinating, as was the evidence you brought to back it up- one of the betazoid scientists was thrilled to meet this Korob person- that's not the issue here."

"If it's about the Mudd Incident, the security officer that hit him was his wife, now his ex-wife, and it was a family squabble so-."

"Kirk, why do you have an unregistered Alien creature from M113 on your ship?" Pike cut across what was undoubtedly going to be another long and slightly insane story.

"Saline is now the last of her kind, and she begged for asylum. I do have the right to grant such a thing."

"To enemies of the federation that wish to defect."

"That is not outright stated, and in fact, the regulations do allow-."

"Mr. Spock, when I wish to be informed of the technicalities, I will ask." Pike cut across the other, looking annoyed. "You have this, 'Saline' as part of security?"

"All she wanted was salt and company. She proved to be extremely protective of the children onboard."

"And the creature that attacked you, her … lover?"

"Caretaker, was extremely protective of her, and we had to retaliate when he attacked the landing party, and then disguised himself to attack the ship. Saline also turned on him when he almost harmed Dr. McCoy's child."

"I see." Pike picked up the report. "You dumped tribbles onto a klingon ship?" _And the Klingon delegates you where hosting allowed this?_ Was the question that would naturally have followed.

"It seems Kobor had a dispute with another Klingon onboard Koloth's ship. A question of honor, and it seems that duels to death are not the only ways of settling such, disputes. We really couldn't keep all the Tribbles, sir." Kirk explained.

"And what is this about a possible Klingon Civil War?"

Kirk hesitated, before picking a spot on the wall behind Pike's head. "I am sorry sir, that was mere speculation and should not have been included in an official report, please, disregard it."

"Kirk?" Pike frowned.

 _You must understand, this is a delicate matter, swear to me you will not tell anyone what I will tell you._ Kirk took a deep breath. "Chris." He met the other's eyes. "I cannot reveal anything told to me in confidence, outside of my duty as a Starfleet Captain."

"Jim … you do have a duty to inform Starfleet of any danger to it, the Federation, or its interests, regardless of whatever Klingon-honor vow you swore to."

"I can only officially speculate, sir, that this possible dissent in the Klingon Empire, will not be a danger to the Federation." Kirk looked at Pike. "Unofficially, Chris, this is something you might wish to ask Major Worf or the Klingon Ambassador about, without listening ears."

"Your opinion, then, Mr. Spock?"

"My opinion, Admiral, is that the Enterprise did not get much information of this possible, dissent, to form an accurate or precise conclusion. It is, of course, entirely up to Starfleet on how to handle this speculation."

Pike noticed the way Kirk had shifted slightly while Spock was speaking, as if to try and silence him, before stopping. "I take it you did not swear a vow, Mr. Spock?"

"I did not need too, Vulcans do not like speculation."

Pike sighed. "Well, I suppose 'speculation' is not really much to go on, but the instant you get a fact, I expect you to give me that information. This alliance is weak as it is."

"Understood, sir." The two saluted and left, Pike watched them go with a little amusement. Neither had actually agreed to give any future information.

* * *

"Captain, the Admiral does have a point." Spock began as they walked to a car. "Things are tense even in the federation due to those who dislike the Klingons, the fact that something similar is happening to them is not illogical."

"I'm well aware of that, Mr. Spock." Kirk took the driver's side with a sigh. "I am also aware that the Admiralty and anyone with half a brain would realize it as well."

"Then why hide the details?" Spock frowned as Kirk started driving to the small room they were sharing while the Enterprise was being checked for damage done to her hull via the transmuter.

"Because the Klingons insist this is a private matter, and don't want the Federation or Starfleet interfering; I happen to agree with that."

"You think someone will use it as an excuse to destroy the alliance, then?"

"Most logical scenario, don't you think?" Kirk sighed. "And that's not forgetting the Romulans. Two of their enemies have teamed up, they won't want us to continue working together."

The chime of a Padd had Spock briefly distracted. "Orders. We're to escort several Delegates and Ambassadors to the planet of Babel once the last checks are done."

"… I'm going out on a limb and guess they want to discuss the alliance with the Klingons?" Kirk knew he was not going to like this mission.

"It appears our neutrality on the issue was the deciding factor on which ship the Klingon Ambassador will travel on."

"Speculation, Mr. Spock?"

"Logical Reasoning, Captain." Spock corrected, studying the mission parameters. "There are two other ships escorting the delegates to Babel, Captain Decker is known to have lost family to the Klingons, while Captain Tracey requested not to transport them."

"Anything else I need to know?"

"… Selek has been requested by the Federation Council to speak on certain events that happened in his timeline. We are to pick him up along with the Organian diplomat on Organia."

"Organia?"

"He thought there was a possibility for them to know a way to get him home."

Selek had wanted to become a hermit, but the federation council had been made aware of the conversation with Nero, and while everyday people weren't aware of the details of what had happened, it was known that the attacker had been a Romulan trying to get revenge on a Vulcan. The council had offered him anything he needed to try and return home, if he wished, and rather than risk being dragged into the spotlight, he'd agreed.

Kirk didn't respond for a moment, pulling into the parking spot outside their room. "So, we've got Klingons, an Older Alternate version of you, and an ambassador from a planet I thought was on the too-primitive-for-contact list. Who else should I be concerned about?"

"Ambassador Sarek and wife for Vulcan, and Admiral Marcus is sending one of his aides, Commander John Harrison."

"Background?"

"Classified for the most part, the only back ground I can find is he's a Special Operations Agent with a background in weapons development."

"… Doesn't sound like someone you want on a diplomatic mission." Kirk frowned.

"Indeed not … shall I inform security?"

"I'll have Lieutenant Rand call a command meeting at 2100 hours. Final Check will be happening then." Kirk looked at Spock. "Meanwhile, see what non-classified information you can get on our guest-list and send it to Giotto."

"Understood." They exited the car, and reluctantly began preparing for what already looked like a difficult mission.

* * *

 **Short opening, I know, just needed to get something out there, will be updated in a week or two, depending on real life and the muse in a blue science dress who is still grieving.**

 **Yeah, Classified files don't 100 percent redact everything, just whatever is above your rank- a civilian and yeoman would just get a name and the word classified. Kirk and Spock are high enough on the chain to get name, rank, and the specialty on file, nothing on the actual weapons designed, or where he worked previously. Naturally, a diplomatic mission, you don't want to hear 'weapons development'.**

 **Or at least that's sort of naturally logical to me, thoughts?**


	2. Chapter 2

**Sorry for the delay, the loss of Nimoy hit my muse and my beta hard. So, here we go ... I, uh, managed to annoy my beta with part of this chapter.**

 **Warnings: This is a FRIENDSHIP fic. That means NO ROMANTIC FOCUS. Also, ALTERNATIVE CHARACTER INTERPRETATIONS!**

 **Edit 12/14/15: I keep watching these movies half-asleep, characters tend to get messed up. Namely, despite my notes, I switched the names of Gorkon and Chang. Thanks to Bad Habits who pointed it out.**

* * *

" **Alien Language translated to English.** "

" _Foreign earth language translated to English._ "

"Occasionally, a _Foreign/Alien word_ will be in a sentence."

"Speaking through a Communicator will be underlined."

' _Telepathic speech.'_

 _Thoughts._

* * *

 **"Only solitary men know the full joys of friendship. Others have their family- but to a solitary and an exile his friends are everything." -Willa Cather**

* * *

"I dinnae like this, Captain." Scotty's opinion was shared by Uhura.

"There's something odd about the syntax of the orders regarding this Commander Harrison." She frowned at the Pad. "It's almost like a veiled threat, that he's to accompany us for security purposes … but the threat could be to the passengers or the crew equally." Uhura sighed. She was good at languages, and Kirk had started her on working out Codes with Giotto almost the day she was confirmed as Chief Communications Officer because too often new languages included veiled threats to the crew's safety.

"I'm aware of that, Lieutenant, this meeting is to evaluate the possible procedures to deal with any sabotage to the mission, internal or external."

"Does ze Keptain already have a plan?" Chekov asked, looking eager.

"Other than informing Harrison I'll be watching him and having you all tell me how he behaves around passengers and crew, we need a security team to guard the Ambassadors and their entourages the instant something happens. Security may have to pull double duty." Kirk looked at Giotto, who nodded.

"I'll get the schedules drafted up. Saline will want to stay with the children, and I think Ensign Stella will want to stay with her. They work well together. More than a few of my boys like Kobor and Bo'rak, so they'll be able to keep the klingon delegation safe from those that have issues, not that there are very many after that Tribble incident." Giotto tapped his fingers on the arm of his chair. "My issue is this Commander Harrison, however, as pointed out, it might be nothing, but if all of us are having a problem with this man's appearance on board, the crew will pick it up from us, so I advise we don't act on our suspicions."

"And alerting Harrison to your own suspicions would be unwise, Captain." Spock added. "If he is a threat to this ship and crew, alerting him of your suspicions will make you his first target." Spock paused, and then sat up even straighter in his chair (if that was possible, he'd already been ramrod straight). "Making yourself his first target is a poor plan, Captain, I strongly suggest you do not do that."

"I'm with Spock on this one," McCoy agreed, and glared at Kirk, "Don't even think about it."

"It's perfectly likely that Commander Harrison is not a threat, and we're jumping at shadows." Kirk retorted, only for Rand to pass him a Padd.

"Admiral Marcus, sir, he wants you to come to his office to meet with him and Commander Harrison alone regarding the man's assignment." Rand leaned back to cross her arms. "If you'll permit, I believe the past missions have proven our instincts on the motivations of others have been uncannily accurate, Sir."

"Your observation is noted, Lieutenant. We will go with Giotto's plan for now. Mr. Spock, I trust you will have everything prepared for when I return?"

"Yes, Captain." Spock watched him go, knowing full well his brother and captain would most likely make sure to draw Harrison's attention to him rather than let a threat to his crew pick his own target.

* * *

If he did this, they would unfreeze one of his crew, Admiral Marcus had assured him, and take the rest out of the torpedoes.

A blatant lie, of course, but Khan had no choice. His only other option would be to run and abandon them to certain death, and Marcus would make sure he knew about it. Make sure he saw one of the torpedoes hit. He wasn't that desperate yet, he could be patient a little while longer. Though every time he looked in the mirror, he regretted it. They'd changed him, in order to not arouse suspicion, supposedly, but it didn't change the fact he was now different- would his crew even recognize him? Eventually, he would appear as he used to, but the technique used had guaranteed it would hold for at least a decade, maybe longer.

He studied the dossiers on each member, studied what little they had on the Klingons. The Captain and the First Officer were an interesting read, as a child the captain had kept others safe in a genocide, the First Officer having been among them, and who had deferred leadership to the younger male. Khan found most of the information of that time period on the first officer buried, but it wasn't hard to connect the dots.

Over 200 years, and humans were still killing each other. Khan found it ironic, given his treatment at the hands of Admiral Marcus and Section 31. The only ones Kirk had lost had been physically weakened by malnutrition and illness, none of them had been killed by soldiers.

Khan's fascination only built as he read about the man's intelligence (Communications Doctorate, Navigation and History Masters, Computers and Engineering Majors … impressive) and his track record of missions (even those that were considered failures had the man responible for saftey of the survivors). Even without the Vulcan by his side, the young man had been clever enough to survive some rather close calls.

The rest of the crew was just as an intelligent, the Chief Pilot was working on his doctorate in Xeno-botany, the young navigator was a certified child genius with two navigational doctorates and three more on trans-warp sciences pending, the Communications officer could speak multiple languages fluently (32 and counting) and could figure out what she didn't know quickly (she had been able to translate some old alien language that had baffled the inhabitants of that planet). The engineering officer, third in command, was a certified genius in engineering, and was mentoring an Orion female (her body phermones would be a possible problem, he had not been exposed to the phermones of orions before) that showed promise with her own doctorate in computer engineering pending.

But it was the Captain that held the most fascination for him, and he hid his curiousity as Marcus buzzed for him to enter the meeting.

"Commander Harrison, this is Captain James T. Kirk." Admiral Marcus introduced them, and Khan studied the shorter man for a moment, easily slipping into the role of Commander Harrison.

"Captain, it will be an honor working with you."

"Likewise, I'm sure, Commander." Kirk nodded, and then looked at Admiral Marcus. "Though I'm curious as to why you're accompanying us?"

"Extra Security, Kirk." Marcus answered easily. "Starfleet doesn't want any trouble with those Klingons, and Harrison will be the best man for the job."

"I see. Then we depart at 1900."

"I'm ready to come aboard now, Captain." Khan assured him, and Kirk nodded.

"Very good commander."

"Kirk, you'd do best to remember what I said." The Admiral added as he walked them out of his office.

"I will keep it in mind." Kirk gave a salute, and continued walking out. Khan followed, easily keeping pace as he grabbed the bag that he'd brought with him. "So, why are you really accompanying us?" Kirk asked conversationally as they made their way to a transporter pad.

"Extra Security, Captain."

"Harrison, let's get one thing clear, I don't particularly care what the Admiral has planned. If it puts my crew in danger, there will be no place you can run from me." Kirk didn't even stop and look at him, or drop the conversational tone. "Understood?"

"Aye, Captain." Khan kept his face straight. It was amusing that Kirk thought he would kill him, and he lost a few points for letting him know he was suspicious of him right at the start, but Kirk was also letting him know that he could be a potential ally- his psychological exam had rated him rather high on being protective of those he cared about, dangerously so, one evaluator had felt.

The instant they materialized on the pad on the ship, Kirk was accosted by one of the Klingons that had been stationed onboard.

"Major Worf, has Ambassador Gorkon arrived?"

"Yes, but there's been a complication you should know." The Klingon answered.

"Of course there has, what is it?" Kirk absently introduced them, and Khan wondered why Kirk had not dismissed him.

"He brought his young daughter with him." Maj. Worf explained. "His wife died, recently. Saline was part of the security detail that greeted them, and well, her powers are more subconscious, at times."

"So, he saw his deceased wife, and I guess Saline quickly adopted the child?"

"Yes, Captain. He demands to speak with you immediately."

"Where is he now?"

"Meeting room Alpha." The Major answered. "Commander Spock is with him."

"Then I'll go with you. Yeoman Barrows!" A female security officer turned and looked at him. "Escort Commander Harrison to his quarters, and give him a tour of the ship. Commander, I will see you on the bridge at 1900." The Captain walked off with the Klingon.

"This way, Commander."

The tour only really showed the parts of the ship that he'd need to find in a hurry, the medical bay, the brig (he found that amusing), the gym, the mess and the bridge, with directions to other places he might want to see, such as the observation decks. The security officer was polite as she led him back to his quarters before leaving.

Khan studied the temporary quarters for a moment, before quietly unpacking his things. He had, roughly, a month before they started their approach to Babel, a month of gathering information and deciding who would be the best to kill to start the war Marcus wanted.

A month to find a way to let Kirk in on the secret, and see just what the Captain would do when he found out the Admiral's plan. Khan smiled, Marcus had made a grave mistake introducing them, Kirk's file had more than one comment on disobeying orders to protect or help those that asked for it, after all, and Khan knew the other Captain would sympathize with him if he played his cards right.

* * *

"That, Saline, you say, is the last of her kind?" Ambassador Gorkon frowned, still not happy with having been greeted with the form of his deceased wife, or the way that creature had cooed over his daughter.

"Yes. She requires a very specific diet of salt and companionship, which they used to get by taking the form of someone that another loved, like a changeling. Most of us care for her as she really is, which Saline says is actually better than the emotions she got when she pretended to be someone. Your love for your wife, Ambassador, must've been the strongest she's been near, to have her powers slip in such a way." Kirk explained. "As for her care of your daughter, the more, definite, someone feels for a person, the better she can relate to the form she takes. Combine the memory of your wife to someone who is the last of her kind, who believes children must be protected at all costs … that is the reason she's primarily the guard we have for the children on board."

"Your First Officer said something to that affect, also that she had proven herself to be loyal." The Ambassador nodded, considering.

"If I may, she's more than proven herself, Ambassador." Worf spoke up, gaining an odd look from Kirk. "We've spoken to you of the, incident, with Kor- Saline took out seven strong warriors just because they made one child cry."

"Ah, yes, Kor, that's something I need to inform you of, Captain Kirk."

"Ambassador?"

"If I may be assured of no listening ears?"

"Computer, Whitewash protocol, 2-5-7-4-3-8-4-3-Alpha-November-Baker." There was no response from the computer. "Six point 32 minutes before the normal records resume, Ambassador." Kirk had thought only Vulcans could raise an eyebrow in that manner.

"Yes, well. Kor has turned on the empire. He believes our treaty with the Federation a grave insult to our honor, and, we believe he is not the first. Opinion is divided on how to deal with them, at this moment."

"There's very little I can do about it, Ambassador."

"There is, one thing, I would ask from you, no matter how this turns out." Gorkon paused, wondering how to phrase it, before deciding to be straight forward. "Protect my daughter. The future rests on our children, Federation and Klingon, so that someday, we may join together. I would have her be a vision of that very future."

"The Enterprise will protect her, Ambassador."

"My thanks, Captain Kirk."

* * *

Saline hummed as she watched the children play in the children's gym. The klingon child, Azetbur, was following Joanna around, mostly because Joanna was the only one who somewhat understood her language and culture.

"Makes you wonder about having a rugrat of your own, don't it?" Stella Mudd (until the paperwork for changing her name came through) was also watching the children. Normally, she kept an eye on any cadets or interns assigned to the ship, but as they were planet-side for a little longer, her matronly duties included watching the younger children until it was time to depart.

"We've yet to find any species that's a biological match for me, though." Terrans, or Humans, were fortunate, they were biologically compatible with many species, though some matches did need some help from science.

"And there are how many trillion species? Give it time, we'll find something." Stella waved a hand. "You've got us, anyway."

"That I do, Stella. Thank you." Saline nodded, watching as the children's teachers gathered them up to head back to the schoolroom. The instant she stepped out the door, however, she felt her camoflauge try to come up, and she stiffened. There was someone, someone wrong, impressions so strong and yet weak at the same time. "Stella."

"I see him, stand with the children."

* * *

Khan had been unable to remain in his quarters for the hour and half till take off, that he'd decided to wander the ship. He had not been expecting one of his crew to step out, except the form kept changing between them. 'Not real', he'd realized wondering if this was the 'Saline' creature that had been discussed, but a small woman walked over to him as the form backed up.

"Identification." The woman asked, and Khan passed the i.d. that Marcus had assigned to him. "Commander, You're a bit off the beaten path."

The woman reminded him of one of the minders they had back when they were being made into supermen. Not enhanced, but frightening enough that none of them dared test her. "My apologies, I received the tour earlier, but I wanted to familiarize myself a bit more."

"You gave Saline a fright." The security officer frowned. "She's the one that's green furred, small mouth with sharp teeth, and vaguely female."

"I, see?" The shapeshifter, Khan remembered, the creature Marcus wanted to know if it would work for them, given the proper incentive. "Oh, my apologies."

"In the future, Commander, please check before you wander. We take the security of our children seriously."

"Of course, I did not mean to cause any trouble." Khan was surprised to see the creature described in an ill fitting red security dress, holding the hand of a young girl, who was holding the hand of a little klingon, a puppy tagging along at their heels.

"Hmph, see that you don't." The woman turned and walked back to the children. "And you'll want to be on the bridge a few minutes prior to leaving. Lift is over there."

Khan nodded, and walked to the lift. Kirk had children aboard, that would make it far more difficult to appeal to Kirk's protective nature.

* * *

 **Children on Starships- let's see, five year missions, large ships, unreasonable to not have families and children aboard, especially as accidental pregnancies might happen. We see them in next generation a bit more, but the fact remains, children are there on board. Rule of action means you don't pause too long to show how those things work, but I'm breaking that rule, because it does add an extra layer, which, because I've almost completely re-written this, is important.**

 **Stella Mudd takes shit from no one. She's much happier now that she's gotten her divorce, and when the paperwork goes through to get her maiden name back, she'll be even happier. She and Saline have apparently become gal-pals, too. Not sure how, yet.**

 **Khan and Saline will have an actual discussion later on. He's going to be struggling the entire time, though.**

 **Gorkon- he's the guy Kirk gets framed for killing in Undiscovered Country. Thanks to Bad Habits for his daughter's name.**

 **Kor- told you he'd show up.**

 **And yes, Kirk has gotten the confidence of a couple Klingons- Four adults, and eventually one child. That's pretty much it.**


End file.
